SPECIFIC ACTIVITIES OF THE GNOTOBIOTICS and MICROBIOLOGY CORE A. Core Services Core services are provided on a charge-back basis. They are designed to achieve economies of scale for purchase of equipment, reagents/supplies, and labor so that the real costs of use are subsidized by up to 50% for individual investigators. 1) Maintenance of Germfree mice: The core maintains germfree mice for a number of investigators, including wild-type Swiss Webster and C57BL/6 strains, as well as knockout strains that have been derived for investigators by Taconic or other sites. Mr. Yeliseyev manages isolators for 4 investigators who use core isolators on a regular basis. Ms. Belavusava assists in microbiological sterility checks of mice, as performed by culture and 16S rRNA PCR. 2) Maintenance of Specifically-Associated Mice: The core has 4 small positive-pressure isolators for specific-association experiments with commensal organisms. The Core Director and Mr. Yeliseyev work with investigators to devise experimental plans for specific-association experiments and schedule use of isolators. 3) Maintenance of Specifically-Associated Mice with BL-2 pathogens: The core has 2 negative-pressure isolators for association of germfree mice with BL-2 pathogens alone or with commensal species. Mr. Yeliseyev, with assistance from Ms. Belavusava, maintains isolators with specifically associated mice while Ms. Belavusava assists with culturing of isolates for associations and quantitative culture of materials from colonized mice, as warranted. 4) On-site breeding and availability of wild-type germfree stocks: The core maintains 2 large breeding isolators, primarily to provide a local supply of germfree Swiss-Webster and C57BL/6 mice for experiments. Local breeding provides a significant savings in animal purchase costs to HDDC investigators (>70% savings) and often provides a more ready supply of wild-type mice than can be obtained from commercial sources. Per request, the core will also maintain small numbers of breeding pairs of other strains of germfree mice imported by HDDC investigators for designated experiments. Mr Yeliseyev maintains animal breeding colonies, including ordering commercially-maintained germfree mice to replenish breeding stocks as needed. Note, Core E does not currently undertaking germfree derivations given space constraints in available mouse facilities in the Longwood area. The core does provide information and options for deriving mouse lines to a germfree state through Taconic or Charles River. HDDC: Integrated Epithelial and Mucosal Biology Lencer, Wayne I. 5) Tissue harvest and histopathology: The core offers assistance with collection of mouse tissues and blood, and preparation of materials for frozen section or paraffin embedding. Mr. Yeliseyev is well-versed in animal dissection and is available to perform or otherwise assist investigators with tissue harvests. Dr. Bry is also able to assist and advise with optimal methods to perform mouse necropsies for downstream applications. 6) Aerobic and anaerobic culture: The core provides equipment, materials and expertise for the culture of aerobic, microaerophilic and anaerobic species. Resources are available in Dr. Bry and Dr. Onderdonk's labs and may be further supported through additional technical staff in their labs. 7) Microbial identification and analysis: The core has equipment, resources and expertise to speciate commensal isolates by microbiological, biochemical and molecular methods, including biochemical analyses of fermentation profiles and other enzyme activities, MIDI analysis of short- medium- or long-chain fatty acids, and comparison of 16S rRNA sequences against curated 16S libraries. 8) Analyses of the Microbiome. The core has the resources and expertise to assist investigators with the collection and preparation of human and rodent samples for deep sequencing of 16S rRNA gene signatures. HDDC investigators may access bioinformatics tools maintained on the BWH High Performance Computing Cluster for analysis of Roche 454 sequencing data of 16S rRNA gene signatures.